{"id":22731102,"url":"https://github.com/genentech/pviz-app-proteomics-3d","last_synced_at":"2025-03-30T01:29:51.405Z","repository":{"id":14516246,"uuid":"17230105","full_name":"Genentech/pviz-app-proteomics-3d","owner":"Genentech","description":null,"archived":false,"fork":false,"pushed_at":"2014-04-18T21:48:01.000Z","size":356,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":16,"default_branch":"master","last_synced_at":"2025-02-05T03:27:56.382Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-02-26T23:50:28.000Z","updated_at":"2015-01-06T19:29:24.000Z","dependencies_parsed_at":"2022-08-27T07:51:36.516Z","dependency_job_id":null,"html_url":"https://github.com/Genentech/pviz-app-proteomics-3d","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpviz-app-proteomics-3d","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpviz-app-proteomics-3d/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpviz-app-proteomics-3d/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpviz-app-proteomics-3d/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/pviz-app-proteomics-3d/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246264489,"owners_count":20749473,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-10T19:19:27.336Z","updated_at":"2025-03-30T01:29:51.384Z","avatar_url":"https://github.com/Genentech.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pViz.js/VEP viewer: A browser side only application to view 2D and 3D proteomics features\n\nThis application displays proteomics data (Peptide/Spectrum matches and PTM quantification information) and ties them to 3D structures read from PDB files. It is aimed at being a demonstration of the capabilities of the \u003ca href=\"http://github.com/genentech/pviz/\"\u003epViz JavaScript library\u003c/a\u003e to display customizable protein features on the sequence.\n\nThe demo protein is [ERBB2_HUMAN](http://www.uniprot.org/uniprot/P04626), where both the PSM and PTM have be randomly assigned.  PDB and sequence is parsed from the Uniprot text file via the [Uniprot.js JavaScript library](http://github.com/genentech/uniprot-js).\n\nCheck the help menu to have more details on usage.\n\nThe application can be used live at [http://research-pub.gene.com/pviz/app/proteomics-3d](http://research-pub.gene.com/pviz/app/proteomics-3d)\n\n**Warning:** you must have a WebGL enabled browser to benefit fully from the application (beware of older Internet Explorer and Mac OS X versions).\n\n## Data source\nUniprot text file is downloaded dynamically from [Uniprot web site](http://www.uniprot.org/uniprot/).\nOnce a 3D structure is selected, the PDB file is downloaded from the [Protein Data Bank](http://www.rcsb.org) web site.\nBoth theses files are parsed in JavaScript to extract the meaningful information.\n\nFor the example, PSM and PTM information reside in 2 TSV files stored in the data directory (information was populated randomly).\n\n###How to adapt the application?\nAn effort was made to decorrelate data from the application.\nIt is straightforwards to replace the protein id and the proteomics information sources by other ones.\n\n##A note to developers\n###Run it locally\nClone the project, then\n\n    npm install\n    bower install\n\n    #if grunt was not installed with -g\n    alias grunt=./node_modules/grunt-cli/bin/grunt\n\n    grunt server\n\nEt Voilà\n\n###Deploy\n\n    grunt build\n    rsync --recursive --delete dist/* your.host:/your/path/\n\n###A note on GLmol.js\nAlthough GLmol.js was a key component of this application, we had to [fork](https://github.com/alexmasselot/glmol\") it and make it compatible with more recent versions of [Three.js](http://threejs.org/) (thanks to the authors for their help on that path).\n\n##Authors\nThis application is based on the versatile [pViz.js: a dynamic JavaScript \u0026 SVG library for visualization of protein sequence features](http://github.com/genentech/pviz) JavaScript library, written by \u003ca href=\"mailto://masselot.alexandre@gene.com\"\u003eAlexandre Masselot\u003c/a\u003e and \u003ca href=\"mailto://mukhyala.kiran@gene.com\"\u003eKiran Mukhyala\u003c/a\u003e, from the Bioinfromatics \u0026 Computational Biology Department, at [Genentech Inc.](http://www.gene.com) Research.\n\n##Reference\nPlease provide a reference to this application by citing:\n'''xxx.xx 2014'''\n\n##Thanks to\nThis app is aimed at demonstrating pViz library.\nBut it would never have existed without a myriad of other useful an inspiring projects:\n[d3.js](http://d3js.org), [color brewer](http://colorbrewer2.org/),\n[GLmol.js](http://webglmol.sourceforge.jp/index-en.html) (and more precisely the [forked](https://github.com/alexmasselot/glmol) version to work with recent [Three.js](http://threejs.org/)),\n[grunt](http://gruntjs.com/),\n[bower](https://npmjs.org/package/bower),\n[bootstrap](http://getbootstrap.com/css),\n[jQuery](http://jquery.com), [backbone.js](http://backbonejs.org),\n[require.js](http://requirejs.org), [underscore.js](http://underscorejs.org).\n\n\n###Continuous integration\nMinification, distribution etc. can be launched in a CI environment via ant tasks (./build.xml)\n\n###Authors\nThis library was initiated by\nAlexandre Masselot (masselot.alexandre@gene.com) \u0026 Kiran Mukhyala (mukhyala.kiran@gene.com) within Genentech Bioinformatics \u0026 Computational Biology Department.\n\n###License\nThe library is distributed under a BSD license. Full description can be found in [LICENSE.txt](LICENSE.txt)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fpviz-app-proteomics-3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fpviz-app-proteomics-3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fpviz-app-proteomics-3d/lists"}